Bug: Holy moly. Figured out that on a Linux system, for some reason unbeknownst to me, using a FileReader to pass into Apache's IOUtils' copy() method to copy to a ZipOutputStream truncates the size of the files that end up in the Zip. This issue does not occur on the Mac. 

Ended up switching FileReader to FileInputStream and everything works fine on Linux
Merge remote-tracking branch 'upstream/master'
Merge pull request #7 from isuftin/master

Zip fix